I agree that doesn't look how I would want.
Are you using the same type of thread top and bottom? With my friends long arm we got much better results with prewound bobbins of a different thread weight (lighter) than we used on top. We never could get her machine to wind a decent bobbin either while running or not.
I have a vintage Pfaff that is my go-to machine for costuming and fancy threads/fabrics but I could never get it to do a decent quilt stitch. Oh the piecing was find but no, couldn't get the stitches to meet in the middle despite hours/weeks/months of fiddling.
But yes, a lot of that does get sucked in during the wash/dry process. I'd try the do a sample and wash it and see how it looks. Also try a couple of different battings with your settings the same and see how they react.